Creating and updating templates

Adding new templates

If you would like to submit a new template or replace an existing one, please submit an issue on GitHub including:

1. A FASTA or BPSEQ file with a reference sequence and secondary structure - see FASTA and BPSEQ examples

2. A Traveler XML file - see example

3. Description of the new template and any relevant background information

:warning: GitHub currently does not support attaching files with .fasta or .bpseq extensions so please attach the files as .txt.

We will review the template and reply on GitHub as soon as possible.

Manually creating templates

Creating templates using FASTA/BPSEQ and Traveler XML files

1. Place new FASTA or BPSEQ file(s) in the data/new folder

2. Run r2dt.py generatecm. The command will generate new .cm file(s) with the covariance models

3. Move the new .cm and .tr files in the destination directory (for example, ribovision-ssu is where all SSU templates submitted by the RiboVision group are stored)

4. Run r2dt.py generatemodelinfo <destination>/cms to add new models to the list of searched models where <destination> is the same folder as in the step above

5. Update metadata.tsv file in the destination directory

6. Run r2dt.py list-models to update a list of all available models

7. Verify that the templates work as expected by testing on a fasta file with a sequence similar to the template

8. Run tests and update the model counts in TestCovarianceModelDatabase as needed

Creating templates using RNA 2D JSON Schema files

It is possible to generate new templates using RNA 2D JSON Schema files as input.

1. Generate a structure using R2DT on the command line and locate the JSON output file

2. Upload JSON file to an interactive editor

3. Manually edit the layout

4. Download the edited structure as a new JSON file and save it in the data/new folder

5. Run the following command:

   r2dt.py generate-template data/new/<input.json>
   

6. The new Traveler template, covariance model, and a fasta file will be generated in the data/new folder.

Other ways of creating templates

• One can also create new templates locally using the generate_cm_library.py script with the FASTA and XML files described above.

• It is also possible to generate a new template using a special version of the XRNA software, XRNA-GT.

Updating Rfam templates

The following procedure should be done after each Rfam release:

1. Recompute all Rfam templates (takes ~6h)

   r2dt.py setup-rfam
   

2. Run tests

3. Generate new precomputed library archive

   tar -czvf cms.tar.gz <path/to/new/cms>
   

   The folder should contain 2 subfolders: crw and rfam.

4. Update the precomputed library link in Readme

5. Update a list of available models

   r2dt.py list-models
   

6. ⚠️ Note that the tRNA Rfam Traveler template has been manually edited to match the standard tRNA layout so the automatically generated traveler-template.xml file should be discarded and the current version should be kept.